2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.datamodel;
21 * Defines internal constants for unambiguous annotation of DbRefEntry source
22 * strings and describing the data retrieved from external database sources (see
23 * jalview.ws.DbSourcProxy)
28 public class DBRefSource
31 * UNIPROT Accession Number
33 public static String UNIPROT = "UNIPROT";
38 public static String UP_NAME = "UNIPROT_NAME";
41 * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
43 public static final String UNIPROTKB = "UniProtKB/TrEMBL";
48 public static String PDB = "PDB";
53 public static String EMBL = "EMBL";
58 public static String EMBLCDS = "EMBLCDS";
63 public static String PFAM = "PFAM";
68 public static String RFAM = "RFAM";
73 public static final String GENEDB = "GeneDB";
76 * List of databases whose sequences might have coding regions annotated
78 public static final String[] DNACODINGDBS =
79 { EMBL, EMBLCDS, GENEDB };
81 public static final String[] CODINGDBS =
84 public static final String[] PROTEINDBS =
85 { UNIPROT, PDB, UNIPROTKB };
87 public static final String[] PROTEINSEQ =
88 { UNIPROT, UNIPROTKB };
90 public static final String[] PROTEINSTR =
93 public static final String[] DOMAINDBS =
97 * set of unique DBRefSource property constants. These could be used to
98 * reconstruct the above groupings
100 public static final Object SEQDB = "SQ";
103 * database of nucleic acid sequences
105 public static final Object DNASEQDB = "NASQ";
108 * database of amino acid sequences
110 public static final Object PROTSEQDB = "PROTSQ";
113 * database of cDNA sequences
115 public static final Object CODINGSEQDB = "CODING";
118 * database of na sequences with exon annotation
120 public static final Object DNACODINGSEQDB = "XONCODING";
123 * DB returns several sequences associated with a protein/nucleotide domain
125 public static final Object DOMAINDB = "DOMAIN";
128 * DB query can take multiple accession codes concatenated by a separator.
129 * Value of property indicates maximum number of accession codes to send at a
132 public static final Object MULTIACC = "MULTIACC";
135 * DB query returns an alignment for each accession provided.
137 public static final Object ALIGNMENTDB = "ALIGNMENTS";